GROMACS version: 2020.4
GROMACS modification: No
gmx cluster explains that “reorder the RMSD matrix using Monte Carlo such that the order of the frames is using the smallest possible increments. With this it is possible to make a smooth animation going from one structure to another with the largest possible (e.g.) RMSD between them, however the intermediate steps should be as small as possible.”
I was wondering, after obtaining the reordered RMSD matrix, what is the way to go to create this smooth animation?
Thank you in advance,